Do note that Chanjo is built on some of kind-of tricky dependencies. If you are experiencing any issues, help is just a click away in the [documentation][docs].

## UsageChanjo exposes a composable command line interface. You can always save intermediary files at any stage and customize every option. However, using a ``chanjo.toml`` config and UNIX pipes you can end up with something like:

## DocumentationRead the Docs is hosting the [official documentation][docs].

I can specifically recommend the fully [interactive demo]http://www.chanjo.co/en/latest/introduction.html#demo) complete with sample data to get you started right away.

## Features

### What Chanjo doesChanjo works on BAM alignment files and extracts interesting coverage related statistics. You use a BED-file to define which regions of the genome that you particularly care about. The output takes the shape of an extended BED-file.

An optional final step is to load data into a SQL database. This will aggregate data from exons to transcripts and genes. The database will later work as an API to downstream tools like the Chanjo Coverage Report generator.

### What Chanjo doesn'tChanjo is not the right choice if you care about coverage for every base across the entire genome. Detailed histograms is something [BEDTools][bedtools] already handles with confidence.

## ContributorsRobin Andeer

Luca Beltrame ([lbeltrame]https://github.com/lbeltrame)

## LicenseMIT. See the [LICENSE](LICENSE) file for more details.

## ContributingAnyone can help make this project better - read [CONTRIBUTION]CONTRIBUTION.md) to get started!